Location: Immunity and Disease Prevention Research
Project Number: 2032-51530-026-07-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Aug 1, 2019
End Date: Dec 31, 2020
The overall objective of the project is to determine the association of diet with antimicrobial resistance genes in fecal samples from healthy adults.
ARS is conducting an observational nutritional phenotyping study in which dietary intake, lifestyle factors, and health outcomes are being assessed in healthy U.S. adults (>300). Shotgun metagenomes of fecal samples from 288 participants are being sequenced. The Cooperator and ARS have a long-standing collaboration on the analysis of metagenomes and the relationship between diet and fecal metagenomes. In the lab of the Cooperator, several bioinformatics pipelines have previously been implemented to specifically analyze metagenomes for antimicrobial resistance genes (ARGs). At ARS, bioinformatics studies have been conducted to determine appropriate sequencing depth for ARG detection in adult fecal metagenomes. As the optimal metagenomics analysis for quantification of ARGs is an active area of research, the Cooperator and ARS will work collaboratively to determine the consensus pipeline to be used by both labs. The Cooperator will hire a postdoctoral scholar who will be co-mentored by the ARS PI. The postdoctoral scholar will implement the consensus pipeline and quantify ARGs in 288 metagenomes. In consultation with ARS, the postdoctoral scholar will analyze dietary data and determine their relationship of ARG incidence with dietary intake.